Hello,
I am wondering if there are any available example RNA-seq datasets that need to be normalized in specific ways (btwnLaneNormalization versus calcNormFactors)? If not, and more likely, are there any available methods to simulate RNA-seq datasets that could show why specific normalization (btwnLaneNormalization versus calcNormFactors) are necessary in specific situations?
I have been working with makeExampleDESeqDataSet() from DESeq2, but am unable to simulate RNA-seq datasets that show the necessity of specific normalization in specific situations - for example, needing btwnLaneNormalization in one simulation and needing calcNormFactors in another simulation.
I am a bit lost, and would be grateful for any advice!
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